Internet agencies (the biggies) are HUGE companies, and the cruise lines give them INCREDIBLE deals because they book so MANY customers.
Just a clue, I work for one, and our company (a few hundred people) booked over 750,000 people on Carnival last year. That is more than CARNIVAL booked themselves. Do you think Mom & Pop in the strip mall have that kind of clout for pricing? Plus, many offer 24 hr sales and customer service with a LIVE person. I would avoid the fly by night ones, yes. But a good well known site (yahoo, orbitz, expedia, travelnow, etc) is perfectly fine.